Prior to his hiring at Mississippi State, Mullen served as offensive coordinator at the University of Florida and was also alongside Urban Meyer at Utah, where he was quarterback coach of the Utes during their undefeated 2004 season. He developed quarterback Alex Smith into the number 1 overall pick in the 2005 NFL Draft. After Urban Meyer left to take the head coaching position at Florida, Mullen served as the interim offensive coordinator during Utah's Fiesta Bowl victory over Pitt. During his tenure at Utah, he also recruited and partially developed Brian Johnson, QB who led Utah to 13–0 and Sugar Bowl victory in 2009.[4] He also served as quarterback coach under Meyer at Bowling Green in 2001–02.

On December 11, 2008, Dan Mullen was hired as the head coach of Mississippi State by former AD, Greg Byrne.

Mullen's first recruiting class at Mississippi State was ranked #19 in the nation by Scout.com.[6] and his 2012 recruiting class was ranked #18 in the nation.[7] In his first season as head coach at Mississippi State in 2009, his team went 5–7 against the toughest schedule in the nation.[8]

In 2010, his Bulldog team went 9–4 overall and 4–4 in the SEC including victories over Georgia, Florida, Kentucky, and Mississippi; the four losses came only to teams ranked in the Top 12. Mississippi State capped off the 2010 season by defeating traditional power Michigan in the 2011 Gator Bowl 52–14, and achieved a #15 ranking in the final AP poll.

In 2011, Mullen's Bulldogs entered the year ranked number 19 in the nation, with high expectations. A loss to Auburn in the first SEC game of the year hurt the Bulldogs, and they stumbled into the game vs Ole Miss with a 5-6 record. They defeated the Rebels 31-3, and defeated Wake Forest 23-17 in the Music City Bowl to finish 7-6 on the year.

In 2012, Mississippi State opened with a win over Jackson State, and a win over Auburn, the first time the Bulldogs defeated the Tigers since 2007. Mississippi State had a 7-0 record, and a #13 ranking, entering a game vs #1, undefeated Alabama. MSU lost 38-7, and lost two more to #16 Texas A&M, and #9 LSU. MSU defeated Arkansas, and was looking for a 4th straight win over Ole Miss, who was 5-6 going into the game, similar to MSU the year before. The Bulldogs lost 41-24, and then lost to Northwestern 34-20 in the Gator Bowl to finish 8-5.

Mississippi State entered 2013 looking to quiet their critics. MSU started the year against #13 Oklahoma State, losing 21-3. They defeated Alcorn State, but lost to Auburn 24-20. They would defeat Troy, Kentucky, and Bowling Green, and lose to LSU, South Carolina, Texas A&M, and Alabama to drop to 4-6 traveling to Little Rock, Arkansas to battle Arkansas. MSU won 24-17 in overtime, and was 5-6 entering the Ole Miss game. MSU missed a game winning field goal to send the game into overtime, and Dak Prescott got a 3 yard touchdown run on 4th and 2, giving Ole Miss the ball up 17-10. Bo Wallace fumbled in the end zone, giving MSU the 17-10 victory, and for the first time in school history, a 4th straight bowl birth. MSU would defeat Rice 44-7 in the Liberty Bowl to finish 7-6.

In 2014, Mullen led the Bulldogs to one of the greatest seasons in school history. He claimed his first Top 10 win at Mississippi State, as the Bulldogs knocked of #8 LSU 34-29 at Death Valley. He followed that up by beating #6 Texas A&M 48-31 in Starkville. A week later, they knocked off #2 Auburn 38-23. This propelled them to the top spot in both major polls--the highest ranking in Mississippi State's history, and the highest that any FBS team in Mississippi had been ranked this late in the season in almost half a century. Losses to Alabama and Mississippi ended any hope of a national championship. Ultimately, the Bulldogs finished 10-2--only the second 10-win season in school history. This netted them an appearance in the Orange Bowl, only the second major bowl appearance in school history.

Due in part to the Bulldogs' sterling 2014 season, Mullen is already third on Mississippi State's all-time wins list, behind Jackie Sherrill and Allyn McKeen.